Group‐specific environmental sequencing reveals high levels of ecological heterogeneity across the microsporidian radiation

Abstract

The description of diversity is a key imperative in current biological studies and has been revolutionised by the molecular era that allows easy access to microbial diversity not visible to the naked eye. Broadly targeted SSU rRNA gene amplicon studies of diverse environmental habitats continue to reveal new microbial eukaryotic diversity. However, some eukaryotic lineages, particularly parasites, have divergent SSU sequences, and are therefore undersampled or excluded by the methodologies used for SSU studies. One such group is the Microsporidia, which have particularly divergent SSU sequences and are rarely detected in even large-scale amplicon studies. This is a serious omission as microsporidia are diverse and important parasites of humans and other animals of socio-economic importance. Whilst estimates of other microbial diversity are expanding, our knowledge of true microsporidian diversity has remained largely static. In this work, we have combined high throughput sequencing, broad environmental sampling and microsporidian-specific primers to broaden our understanding of the evolutionary diversity of the Microsporidia. Mapping our new sequences onto a tree of known microsporidian diversity we uncover new diversity across all areas of the microsporidian tree and uncover clades dominated by novel sequences, with no close described relatives.

A new method of metabarcoding Microsporidia and their hosts reveals high levels of microsporidian infections in mosquitoes (Culicidae)

“…The metabarcoding approach proposed in this study can be used for The V5 region is flanked by group-conserved sequences that allowed us to design the CM-V5F/CM-V5R primer set with great specificity towards microsporidian ssu rDNA. Indeed, the specificity of our primers seems to be higher than the commonly used V1F/530R pair applied by Williams et al (2018) Percentage of identity Fraction of scores as low or lower than the score being plotted Fraction of scores as low or lower than the score being plotted V5 region of ssu rDNA (Figure 4). However, recently published first sequence data for the two remaining microsporidian lineages-the metchnikovellid Amphiamblys sp.…”

“…The first attempt to use high-throughput sequencing for microsporidian DNA detection was performed by Williams et al (2018).…”

“…Sometimes, microsporidians are recorded incidentally during a fine structure analysis of their hosts (Radek, Kariton, Dabert, & Alberti, 2015; Ribeiro & Passos, 2006). Many microsporidian species are known only based on unique DNA sequence coding for nuclear ribosomal RNA (hereafter: rDNA; Krebes, Blank, Frankowski, & Bastrop, 2010; Vossbrinck, Andreadis, Vávra, & Becnel, 2004; Williams, Hamilton, Jones, & Bass, 2018).…”

Evolution of microsporidia: An extremely successful group of eukaryotic intracellular parasites

“…For example, a study sampling terrestrial nematodes identified 12 distinct microsporidia species, and C. elegans alone has been reported to be infected by seven different species [19,31,35]. Additionally, environmental sampling has identified dozens of novel species [41,42]. Based on the wide diversity of known animal hosts and the specificity of microsporidia species to infect one or several closely related hosts, it has been suggested that the number of microsporidia species equals the number of animal species.…”

Shared geographic histories and dispersal contribute to congruent phylogenies between amphipods and their microsporidian parasites at regional and global scales

“…Among more than 30 named species and many other unnamed taxa that were found in amphipod hosts, Dictyocoela is the most common genus with about 10 known species (Bojko & Ovcharenko, 2019;Dimova et al, 2018;Grabner, 2017;Grabner et al, 2015;Kuzmenkova, Sherbakov, & Smith, 2008;Quiles et al, 2019;Slothouber Galbreath, Smith, Terry, Becnel, & Dunn, 2004;Williams, Hamilton, Jones, & Bass, 2018; see Table 1 in Appendix S1). However, the known diversity of Dictyocoela seems to be restricted both geographically and in terms of host range.…”